As others have stated, LiFePO4 and AGM do not have the same charging specifics, so cannot combine them. Lithium can be charged at full charge until it reaches the full state, after that it will start balancing. AGM first goes at full charge and nearing 90 % it will lower the charge in order to get to 100 %. So combining them on one charging spec is not going to work.
The good part of Victron is that you can maximize the amps the inverter/charger will draw from your generator. E.g. if your inverter can charge at 200 A maximum you can set it at a lower rate so you will have amps available for cooking, washing etc. If your generator would be able to charge less than what the inverter/charger can accept and you don't lower the charging amps the fuse on your generator will simply blow.
On my boat I have basically 3 different battery banks:
1. Service bank, which is 24 V at 1400 Ah
2. Start battery bank which is 12 V (4 x 75 Ah)
3. Bow and stern thruster plus windlass and that is 24 V (at 150 Ah) again.
The service bank can be charged in 4 different ways. That can be via generator or shore power (via the inverter/charger), the solar panels or via the 24 V alternators on the engines which are regulated using wakespeed. While on anchor the solar panels have more than enough capacity (3 Kwp) to charge the service bank in about 4 to 5 hours after a one night use. Even when there is not enough sun I can go 3 days without charging and normally we have then picked up the anchor to move to a different place during which travel the alternators will charge the house bank again.
The start batteries get charged via 12 V alternators, also on the engine, so when the engines run the start batteries get charged to 100 % again.
The third bank gets charged via a 220 V to 24 V smart battery charger that is connected to the service bank via the inverter. This means that as long as the service bank has enough juice those batteries will get charged. After all, when you come into an anchorage or port you shut down the engines and that would mean the bow thruster batteries would not get charged anymore if I would have hooked them up to an alternator.
All I can say is that I have more than enough Ah onboard to not having to use the generator anymore. I just run it every now and then for the sake of running it, but it is no longer required to charge the batteries or run any of the systems onboard. Also during night passages it is not a problem anymore. In the past I had to run the generator in order to be able to run all the required equipment, but now the 24 V alternators keep the service bank full at all times, they have a max capacity of 400 A and that is much more than required.
Also, since I upgraded from 500 Ah to 1400 Ah I don't need to start the generator for cooking or using the dishwasher or boiler anymore. On the 500 Ah AGM I basically only had 250 Ah available and that meant cooking was not possible, I would drain the batteries to below 50 % if I would take them through the night. After all, on anchor our boat systems (lights, radio, stabilizers, pumps etc) would draw about 15 A per hour, so in one night that could be around 150 - 200 Ah. The remaining 50 - 100 Ah would not be enough for cooking, tv, dish washer or washing machine. Since I changed to 1400 Ah those problems are over. Even when I use 500 Ah overnight, the solar panels can fill up the batteries in 4 to 5 hours.
In all I am very happy with the current set up and can highly recommend this path. I do admit it is a costly affair, but the pros outweigh the cons:
1. no more running the generator in quiet anchorages
2. no need to stay awake because the generator has to charge the batteries at night
3. an increased range because am not burning fuel for the generator anymore
4. generator does not increase in hours anymore, which means it will keep its value and I don't need to replace it.
5. but most important, we can use all the equipment onboard at any time and no need to plan usage of equipment anymore.
For us changing to LiFePO4 has given us much more freedom and has decreased our fuel bill by around 5.000 euro per year and increased our range with around 1200 nm. And that means we can now go from one place with low fuel to cost the next one with low fuel cost without the need of fueling in between. At a saving of 50 cents per liter that is around 1250 euro savings each time we fuel up. We fuel up 2 or 3 times a season, so that is an additional 3000 - 3500 euro savings. Total savings in one season in fuel is around 8000 euro. However, since we don't need shore power anymore the savings have gone up even more. Nowadays they charge between 2 and 3 euro per kwh in a port or marina. We would normally use between 6 and 7 Kwh per day, so each time we have to be in port we save an additional 12 to 21 euro. Not a lot, but we will take it.